# bone

**Repository Path**: liukeweiaway/bone

## Basic Information

- **Project Name**: bone
- **Description**: 2024 paper test
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-07-17
- **Last Updated**: 2025-07-21

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# single cell
This repository archives the pipelines and source codes used in the single cell manuscript.

## Contents
The contents are organized into six main folders. Please feel free to click on any title to view the detailed `README.md`.

1. [2024paper](./2024paper)
    The data used in this project
    - [data](./2024paper/data) # big not in this place
    - [result](./2024paper/result)
    - [scripts](./2024paper/scripts)

2. [ourData](./ourData)
    The data used in this project
    - [data](./ourData/data) # big not in this place
    - [result](./ourData/result)
    - [scripts](./ourData/scripts)

## install  R  4.3.3
### conda
mamba create -n R_singleBone r-base=4.3.3 -c conda-forge -y  
mamba actiavte r_env  
mamba install -c conda-forge r-seurat -y  
mamba install -c conda-forge r-ggrastr  -y  
mamba install -c conda-forge r-devtools r-biocmanager -y  
mamba install -c conda-forge r-irkernel -y  
mamba install -c bioconda -y bioconductor-sva -y  
mamba install -c conda-forge r-readr -y  
mamba install -c conda-forge r-VisCello -y # if false replace github  

BiocManager::install("monocle")   
data.table monocle httpuv igraph XML leidenbase  # install.packages("RCurl")
BiocManager::install("clusterProfiler")  

devtools::install_github("cysouw/qlcMatrix")  
devtools::install_github("qinzhu/VisCello")  

mamba install -c conda-forge r-viridis -y   
mamba install -c conda-forge r-forcats -y   

#### SeuratDisk install  
if (!requireNamespace("remotes", quietly = TRUE)) {  
    install.packages("remotes")  
}
remotes::install_github("mojaveazure/seurat-disk")  

mamba install -c conda-forge r-seuratdisk -y   # glibc 2.34   mamba install -c conda-forge glibc # mamba install -c conda-forge libstdcxx-ng  BiocManager::install("SeuratDisk")  
ldd --version  ## 查看glibc 版本  2.28， 要求glibc>2.34  

mamba install -c conda-forge r-GSEABase -y  # BiocManager::install("GSEABase")  

mamba install -c conda-forge r-ComplexHeatmap -y   # BiocManager::install("ComplexHeatmap")  

#### DoubletFinder  
remotes::install_github('https://github.com/ekernf01/DoubletFinder', force = T)   # https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/184   # https://github.com/chris-mcginnis-ucsf/DoubletFinder/issues/190
修改R包源代码  

mamba install -c conda-forge r-irlba -y  
mamba install -c conda-forge r-AUCell -y  
install.packages("openssl")  
install.packages("curl", type = "source")  
mamba install -c conda-forge curl --force-reinstall  
library(devtools)  
install_github("aertslab/AUCell")  
BiocManager::install("AUCell", force = TRUE)  

options(repos = "http://cran.us.r-project.org")  
BiocManager::install("sva")  
BiocManager::install("clusterProfiler")  
BiocManager::install("HiClimR")  # mamba install -c conda-forge netcdf4  

wget https://cytotrace.stanford.edu/CytoTRACE_0.3.3.tar.gz -O CytoTRACE.tar.gz  
mamba install python=3.10 numpy -y  
pip install scanoramaCT   
sva   HiClimR  

### R 
if (!requireNamespace("BiocManager", quietly = TRUE))  
    install.packages("BiocManager")   

BiocManager::install(c("sva", "Matrix", "Rcpp"))  

devtools::install_local("CytoTRACE.tar.gz", dependencies=TRUE)  
library(CytoTRACE)  
IRkernel::installspec(name = 'r_bone', displayname = 'R(conda r_bone)')  

remove.packages("Matrix")
packageurl <- "https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.3-2.tar.gz"
install.packages(packageurl, repos=NULL, type="source")

# python
mamba create -n pyScBone1 python==3.10 -c conda-forge -y
mamba activate pyScBone1
mamba install pytorch torchvision torchaudio cpuonly -c pytorch -y
mamba install pyg -c pyg -y
mamba install -c conda-forge pymde -y
pip install pymde
mamba install -c conda-forge  omicverse -y
python -c "import omicverse"  ## 验证

mamba install -c conda-forge  seaborn -y
mamba install -c conda-forge  pandas -y

mamba install -c conda-forge  scanpy -y
mamba install -c conda-forge  scvelo -y

python -m ipykernel install --user --name=pyScBone1 --display-name "pyScBone1"